☰ Navigation Tabs
Crystal Structure of Human Kallikrein 5 in complex with Leupeptin and Zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BDG PDB ENTRY 2BDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 291 30% PEG-monomethyl ether, 200 mM ammomium sulfate, 100 mM MES,10 mM leupeptin, soaked with 10 mM zinc chloride, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 5.60
Crystal Properties Matthews coefficient Solvent content 3.24 62.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.532 α = 90 b = 66.543 β = 95.14 c = 39.58 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm MIRRORS 2006-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.25 20 99.3 0.043 45.3 2.9 15429 1 24.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 1 0.345 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BDG 2.3 19.71 14052 14052 692 96 0.21 0.21 0.2135 0.235 0.2381 RANDOM 48.1
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -13.24 -1.79 33.08 -19.84
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.7 c_scangle_it 3.39 c_mcangle_it 2.55 c_scbond_it 2.3 c_mcbond_it 1.5 c_angle_deg 1.4 c_improper_angle_d 0.91 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.7 c_scangle_it 3.39 c_mcangle_it 2.55 c_scbond_it 2.3 c_mcbond_it 1.5 c_angle_deg 1.4 c_improper_angle_d 0.91 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1793 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 31
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling PHASER phasing